Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis
Identifieur interne : 002E06 ( Ncbi/Merge ); précédent : 002E05; suivant : 002E07Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis
Auteurs : Annaliese S. Mason [Allemagne, Australie] ; Mathieu Rousseau-Gueutin [France] ; Jérôme Morice [France] ; Philipp E. Bayer [Australie] ; Naghmeh Besharat [Australie] ; Anouska Cousin [Australie] ; Aneeta Pradhan [Australie] ; Isobel A. P. Parkin [Canada] ; Anne-Marie Chèvre [France] ; Jacqueline Batley [Australie] ; Matthew N. Nelson [Australie, Royaume-Uni]Source :
- Genetics [ 0016-6731 ] ; 2015.
Descripteurs français
- KwdFr :
- Brassica (génétique), Cartographie chromosomique, Centromère (génétique), Croisements génétiques, Gènes de plante, Génome végétal, Génomique (), Haplotypes, Marqueurs génétiques, Polymorphisme de nucléotide simple, Séquences répétées d'acides nucléiques, Séquençage nucléotidique à haut débit, Techniques de génotypage, Éléments transposables d'ADN.
- MESH :
- génétique : Brassica, Centromère.
- Cartographie chromosomique, Croisements génétiques, Gènes de plante, Génome végétal, Génomique, Haplotypes, Marqueurs génétiques, Polymorphisme de nucléotide simple, Séquences répétées d'acides nucléiques, Séquençage nucléotidique à haut débit, Techniques de génotypage, Éléments transposables d'ADN.
English descriptors
- KwdEn :
- Brassica (genetics), Centromere (genetics), Chromosome Mapping, Crosses, Genetic, DNA Transposable Elements, Genes, Plant, Genetic Markers, Genome, Plant, Genomics (methods), Genotyping Techniques, Haplotypes, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Repetitive Sequences, Nucleic Acid.
- MESH :
- chemical : DNA Transposable Elements, Genetic Markers.
- genetics : Brassica, Centromere.
- methods : Genomics.
- Chromosome Mapping, Crosses, Genetic, Genes, Plant, Genome, Plant, Genotyping Techniques, Haplotypes, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Repetitive Sequences, Nucleic Acid.
Abstract
Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from
Url:
DOI: 10.1534/genetics.115.183210
PubMed: 26614742
PubMed Central: 4788232
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PMC:4788232Le document en format XML
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A and C Genomes Revealed Through Half-Tetrad Analysis</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name>
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<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
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<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
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<country xml:lang="fr">France</country>
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<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E." last="Bayer">Philipp E. Bayer</name>
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<country xml:lang="fr">Australie</country>
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</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
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<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name>
<affiliation wicri:level="1"><nlm:aff id="aff5">Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
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<wicri:noRegion>Saskatchewan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
<affiliation wicri:level="1"><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
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<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N." last="Nelson">Matthew N. Nelson</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff6">Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN</wicri:regionArea>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
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</analytic>
<series><title level="j">Genetics</title>
<idno type="ISSN">0016-6731</idno>
<idno type="eISSN">1943-2631</idno>
<imprint><date when="2015">2015</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Brassica (genetics)</term>
<term>Centromere (genetics)</term>
<term>Chromosome Mapping</term>
<term>Crosses, Genetic</term>
<term>DNA Transposable Elements</term>
<term>Genes, Plant</term>
<term>Genetic Markers</term>
<term>Genome, Plant</term>
<term>Genomics (methods)</term>
<term>Genotyping Techniques</term>
<term>Haplotypes</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Repetitive Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Brassica (génétique)</term>
<term>Cartographie chromosomique</term>
<term>Centromère (génétique)</term>
<term>Croisements génétiques</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Génomique ()</term>
<term>Haplotypes</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Séquences répétées d'acides nucléiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Techniques de génotypage</term>
<term>Éléments transposables d'ADN</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Transposable Elements</term>
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Brassica</term>
<term>Centromere</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Brassica</term>
<term>Centromère</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term>
<term>Crosses, Genetic</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Genotyping Techniques</term>
<term>Haplotypes</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Repetitive Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term>
<term>Croisements génétiques</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Génomique</term>
<term>Haplotypes</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Séquences répétées d'acides nucléiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Techniques de génotypage</term>
<term>Éléments transposables d'ADN</term>
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<front><div type="abstract" xml:lang="en"><p>Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from <italic>Brassica</italic>
interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina <italic>Brassica</italic>
60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the <italic>Brassica</italic>
A and C genomes to the reference <italic>Brassica napus</italic>
genome. Gene and transposable element density across the <italic>B. napus</italic>
genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.</p>
</div>
</front>
</TEI>
<double pmid="26614742"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name>
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<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
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</affiliation>
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<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
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</affiliation>
</author>
<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E." last="Bayer">Philipp E. Bayer</name>
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</affiliation>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name>
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<wicri:noRegion>Saskatchewan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
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<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
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</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N." last="Nelson">Matthew N. Nelson</name>
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<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff6">Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN</wicri:regionArea>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
</affiliation>
</author>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Centromere Locations in <italic>Brassica</italic>
A and C Genomes Revealed Through Half-Tetrad Analysis</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S." last="Mason">Annaliese S. Mason</name>
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</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
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<country xml:lang="fr">France</country>
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</affiliation>
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<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
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<country xml:lang="fr">France</country>
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<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E." last="Bayer">Philipp E. Bayer</name>
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<country xml:lang="fr">Australie</country>
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<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A. P." last="Parkin">Isobel A. P. Parkin</name>
<affiliation wicri:level="1"><nlm:aff id="aff5">Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada</nlm:aff>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan</wicri:regionArea>
<wicri:noRegion>Saskatchewan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
<affiliation wicri:level="1"><nlm:aff id="aff3">IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff2">School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N." last="Nelson">Matthew N. Nelson</name>
<affiliation wicri:level="1"><nlm:aff id="aff4">School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="aff6">Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea>Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN</wicri:regionArea>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">Genetics</title>
<idno type="ISSN">0016-6731</idno>
<idno type="eISSN">1943-2631</idno>
<imprint><date when="2015">2015</date>
</imprint>
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<front><div type="abstract" xml:lang="en"><p>Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from <italic>Brassica</italic>
interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina <italic>Brassica</italic>
60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the <italic>Brassica</italic>
A and C genomes to the reference <italic>Brassica napus</italic>
genome. Gene and transposable element density across the <italic>B. napus</italic>
genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.</p>
</div>
</front>
</TEI>
</pmc>
<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S" last="Mason">Annaliese S. Mason</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.</nlm:affiliation>
<country wicri:rule="url">Allemagne</country>
<wicri:regionArea>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
<affiliation wicri:level="1"><nlm:affiliation>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
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<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
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<wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
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</affiliation>
</author>
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</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
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<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
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</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
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</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A P" last="Parkin">Isobel A P. Parkin</name>
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<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
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<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
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<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N" last="Nelson">Matthew N. Nelson</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.</nlm:affiliation>
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<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN</wicri:regionArea>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.</title>
<author><name sortKey="Mason, Annaliese S" sort="Mason, Annaliese S" uniqKey="Mason A" first="Annaliese S" last="Mason">Annaliese S. Mason</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.</nlm:affiliation>
<country wicri:rule="url">Allemagne</country>
<wicri:regionArea>Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Rousseau Gueutin, Mathieu" sort="Rousseau Gueutin, Mathieu" uniqKey="Rousseau Gueutin M" first="Mathieu" last="Rousseau-Gueutin">Mathieu Rousseau-Gueutin</name>
<affiliation wicri:level="1"><nlm:affiliation>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Morice, Jerome" sort="Morice, Jerome" uniqKey="Morice J" first="Jérôme" last="Morice">Jérôme Morice</name>
<affiliation wicri:level="1"><nlm:affiliation>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Bayer, Philipp E" sort="Bayer, Philipp E" uniqKey="Bayer P" first="Philipp E" last="Bayer">Philipp E. Bayer</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Besharat, Naghmeh" sort="Besharat, Naghmeh" uniqKey="Besharat N" first="Naghmeh" last="Besharat">Naghmeh Besharat</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Cousin, Anouska" sort="Cousin, Anouska" uniqKey="Cousin A" first="Anouska" last="Cousin">Anouska Cousin</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Pradhan, Aneeta" sort="Pradhan, Aneeta" uniqKey="Pradhan A" first="Aneeta" last="Pradhan">Aneeta Pradhan</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth</wicri:regionArea>
<wicri:noRegion>Perth</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Parkin, Isobel A P" sort="Parkin, Isobel A P" uniqKey="Parkin I" first="Isobel A P" last="Parkin">Isobel A P. Parkin</name>
<affiliation wicri:level="1"><nlm:affiliation>Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada.</nlm:affiliation>
<country xml:lang="fr">Canada</country>
<wicri:regionArea>Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan</wicri:regionArea>
<wicri:noRegion>Saskatchewan</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Chevre, Anne Marie" sort="Chevre, Anne Marie" uniqKey="Chevre A" first="Anne-Marie" last="Chèvre">Anne-Marie Chèvre</name>
<affiliation wicri:level="1"><nlm:affiliation>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>IGEPP, Institut National de la Recherche Agronomique, BP35327, 35653 Le Rheu</wicri:regionArea>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
<wicri:noRegion>35653 Le Rheu</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Batley, Jacqueline" sort="Batley, Jacqueline" uniqKey="Batley J" first="Jacqueline" last="Batley">Jacqueline Batley</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072, Australia.</nlm:affiliation>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, Brisbane 4072</wicri:regionArea>
<wicri:noRegion>Brisbane 4072</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Nelson, Matthew N" sort="Nelson, Matthew N" uniqKey="Nelson M" first="Matthew N" last="Nelson">Matthew N. Nelson</name>
<affiliation wicri:level="1"><nlm:affiliation>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN, United Kingdom annaliese.mason@agrar.uni-giessen.de m.nelson@kew.org.</nlm:affiliation>
<country wicri:rule="url">Allemagne</country>
<wicri:regionArea>School of Plant Biology and The University of Western Australia (UWA) Institute of Agriculture, The UWA, Crawley 6009, Perth, Australia Natural Capital and Plant Health, Royal Botanic Gardens Kew, Ardingly, West Sussex, RH17 6TN</wicri:regionArea>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
<wicri:noRegion>RH17 6TN</wicri:noRegion>
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</analytic>
<series><title level="j">Genetics</title>
<idno type="eISSN">1943-2631</idno>
<imprint><date when="2016" type="published">2016</date>
</imprint>
</series>
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</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Brassica (genetics)</term>
<term>Centromere (genetics)</term>
<term>Chromosome Mapping</term>
<term>Crosses, Genetic</term>
<term>DNA Transposable Elements</term>
<term>Genes, Plant</term>
<term>Genetic Markers</term>
<term>Genome, Plant</term>
<term>Genomics (methods)</term>
<term>Genotyping Techniques</term>
<term>Haplotypes</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Repetitive Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Brassica (génétique)</term>
<term>Cartographie chromosomique</term>
<term>Centromère (génétique)</term>
<term>Croisements génétiques</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Génomique ()</term>
<term>Haplotypes</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Séquences répétées d'acides nucléiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Techniques de génotypage</term>
<term>Éléments transposables d'ADN</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Transposable Elements</term>
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Brassica</term>
<term>Centromere</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Brassica</term>
<term>Centromère</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term>
<term>Crosses, Genetic</term>
<term>Genes, Plant</term>
<term>Genome, Plant</term>
<term>Genotyping Techniques</term>
<term>Haplotypes</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Repetitive Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term>
<term>Croisements génétiques</term>
<term>Gènes de plante</term>
<term>Génome végétal</term>
<term>Génomique</term>
<term>Haplotypes</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Séquences répétées d'acides nucléiques</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Techniques de génotypage</term>
<term>Éléments transposables d'ADN</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate.</div>
</front>
</TEI>
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